Vidal-Melgosa, Silvia; Hehemann, Jan-Hendrik (2020): Polysaccharide structures in HMWDOM and POM at the North Sea detected by carbohydrate microarray analysis [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.924287, In: Vidal-Melgosa, Silvia; Sichert, Andreas; Hehemann, Jan-Hendrik (2020): Polysaccharides present in HMWDOM and POM during a microalgae bloom period in the North Sea [dataset bundled publication]. PANGAEA, https://doi.org/10.1594/PANGAEA.924288
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Abstract:
Here, we traced the abundance of 27 polysaccharide epitopes in dissolved and particulate organic matter along a three month diatom bloom period in the North Sea. We used a bioanalytic approach based on carbohydrate microarrays and monoclonal antibodies (mAbs).
Details describing the data:
Carbohydrate microarray data show the relative polysaccharide abundance (antibody signal intensity) detected in samples harvested during a spring phytoplankton bloom period (21 sampling dates) in the North Sea (54˚11.3'N, 7˚54.0'E). Samples include high molecular weight dissolved organic matter (HMWDOM) and particulate organic matter (POM). Polysaccharides from all samples were sequentially extracted with the solvents H2O, 50 mM EDTA pH 7.5 and 4 M NaOH with 0.1% w/v NaBH4. A library of identical microarrays was created, each populated with the same time-series of extracted polysaccharides. These microarrays were then individually incubated with polysaccharide-specific mAbs or carbohydrate binding modules (CBMs) as probes, which specifically bind to a single polysaccharide epitope. The binding of probes to polysaccharide epitopes on the microarrays was detected using a secondary antibody coupled to alkaline phosphatase, which converts its substrate into a coloured product, the amount of which correlates with polysaccharide concentration. Antibody signal intensity was quantified and the highest signal value in the data set for HMWDOM and for POM was set to 100 and all other values were normalised accordingly. The temporal dynamics but not the absolute number should be compared between HMWDOM and POM pools as they required independent normalisation since their sampling was different. A cut-off of 5 arbitrary units was applied and all probe profiles where in at least one date an antibody positive signal (value ≥ 5) was detected are included in the data set. The epitope recognised by each probe is shown at the top of each column and the name of the corresponding mAb or CBM is depicted in parentheses. Size fractions correspond to: POM 10 µm, over 10 µm; POM 3 µm, between 10 and 3 µm; POM 0.2 µm, between 3 and 0.2 µm; HMWDOM, between 0.2 µm and 1 kDa. HG, homogalacturonan; DE, degree of esterification; AGP, arabinogalactan protein; GlcA, glucuronic acid. This microarray data set reveals the temporal dynamics of 27 polysaccharide epitopes in HMWDOM and POM.
Keyword(s):
Related to:
Vidal-Melgosa, Silvia; Sichert, Andreas; Francis, T Ben; Bartosik, Daniel; Niggemann, Jutta; Wichels, Antje; Willats, William G T; Fuchs, Bernhard M; Teeling, Hanno; Becher, Dörte; Schweder, Thomas; Amann, Rudolf; Hehemann, Jan-Hendrik (2021): Diatom fucan polysaccharide precipitates carbon during algal blooms. Nature Communications, 12(1), https://doi.org/10.1038/s41467-021-21009-6
Coverage:
Latitude: 54.188330 * Longitude: 7.900000
Date/Time Start: 2016-03-15T00:00:00 * Date/Time End: 2016-05-26T00:00:00
Minimum Elevation: -10.0 m * Maximum Elevation: -10.0 m
Event(s):
HelgolandRoads_site (Kabeltonne) * Latitude: 54.188330 * Longitude: 7.900000 * Elevation: -10.0 m * DEIMS ID: deims.org * Location: German Bight, North Sea * Comment: Samples and Measurements were taken at HelgolandRoads site but independently of Helgoland Roads LTER project
Parameter(s):
# | Name | Short Name | Unit | Principal Investigator | Method/Device | Comment |
---|---|---|---|---|---|---|
1 | Material | Material | Vidal-Melgosa, Silvia | Pool + Size | ||
2 | DATE/TIME | Date/Time | Vidal-Melgosa, Silvia | Geocode | ||
3 | Treatment | Treat | Vidal-Melgosa, Silvia | Extraxction | ||
4 | Fraction, description | Fraction desc | Vidal-Melgosa, Silvia | |||
5 | Size | Size | µm | Vidal-Melgosa, Silvia | Size fraction | |
6 | Homogalacturonan with a low degree of esterification | HG with a low DE | Vidal-Melgosa, Silvia | JIM5 | ||
7 | Homogalacturonan partially methylesterified/no ester | HG part methylesterif/no ester | Vidal-Melgosa, Silvia | LM18 | ||
8 | Homogalacturonan partially methylesterified/no ester | HG part methylesterif/no ester | Vidal-Melgosa, Silvia | LM19 | ||
9 | Non-blockwise partially methylesterified homogalacturonan | Non-blockw part methylesterif HG | Vidal-Melgosa, Silvia | LM7 | ||
10 | Calcium cross-linked homogalacturonan | Ca cross-linked HG | Vidal-Melgosa, Silvia | 2F4 | ||
11 | Rhamnogalacturonan I backbone | RGI backbone | Vidal-Melgosa, Silvia | INRA-RU1 | ||
12 | beta-1,4-galactan | b-1,4-galactan | Vidal-Melgosa, Silvia | LM5 | ||
13 | alpha-1,5-arabinan | a-1,5-arabinan | Vidal-Melgosa, Silvia | LM6 | ||
14 | beta-1,4-(galacto)(gluco)mannan | Heteromannan | Vidal-Melgosa, Silvia | LM21 | ||
15 | beta-1,4-(galacto)(gluco)mannan | Heteromannan | Vidal-Melgosa, Silvia | CBM27 | ||
16 | beta-1,4-(galacto)(gluco)mannan | Heteromannan | Vidal-Melgosa, Silvia | BS-400-4 | ||
17 | beta-1,3-glucan | b-1,3-glucan | Vidal-Melgosa, Silvia | BS-400-2 | ||
18 | beta-1,3;1,4-glucan | b-1,3;1,4-glucan | Vidal-Melgosa, Silvia | BS-400-3 | ||
19 | Xyloglucan | Xyloglucan | Vidal-Melgosa, Silvia | LM25 | ||
20 | beta-1,4-xylan | b-1,4-xylan | Vidal-Melgosa, Silvia | LM10 | ||
21 | Xylosyl residues | Xylosyl residues | Vidal-Melgosa, Silvia | LM23 | ||
22 | Glucuronoxylan | Glucuronoxylan | Vidal-Melgosa, Silvia | INRA-UX1 | ||
23 | Cellulose | Cellulose | Vidal-Melgosa, Silvia | CBM3a | ||
24 | Cellulose | Cellulose | Vidal-Melgosa, Silvia | CBM4-1 | ||
25 | Arabinogalactan protein glycan | AGP glycan | Vidal-Melgosa, Silvia | JIM13 | ||
26 | beta-linked GlcA in arabinogalactan protein | b-linked GlcA in AGP | Vidal-Melgosa, Silvia | LM2 | ||
27 | GlcA in arabinogalactan protein | GlcA in AGP | Vidal-Melgosa, Silvia | LM14 | ||
28 | Arabinogalactan protein glycan | AGP glycan | Vidal-Melgosa, Silvia | MAC207 | ||
29 | Fucan | Fucan | Vidal-Melgosa, Silvia | BAM1 | ||
30 | Fucan | Fucan | Vidal-Melgosa, Silvia | BAM2 | ||
31 | Fucan | Fucan | Vidal-Melgosa, Silvia | BAM3 | ||
32 | Fucan | Fucan | Vidal-Melgosa, Silvia | BAM4 |
License:
Creative Commons Attribution 4.0 International (CC-BY-4.0)
Size:
7749 data points
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